Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing

FEMS Microbiology Ecology

Volumn 79, Issue 2, 2012, Pages 371-379

  Murase, Jun ^a   Shibata, Manami ^a   Lee, Chol Gyu ^a   Watanabe, Takeshi ^a   Asakawa, Susumu ^a   Kimura, Makoto ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

DNA stable isotope probing; Fungi; Microbial community; Paddy soil; Protists; Rice callus

Indexed keywords

CARBON; DNA;

CARBON CYCLE; CARBON ISOTOPE; DNA; FUNGUS; ISOTOPIC ANALYSIS; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PADDY FIELD; PLANT RESIDUE; SOIL ECOSYSTEM; SOIL MICROORGANISM; SOIL ORGANIC MATTER; STABLE ISOTOPE; TAXONOMY;

ARTICLE; CHEMISTRY; CLASSIFICATION; DNA PROBE; ECOSYSTEM; EUKARYOTE; FUNGUS; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT; RICE; SOIL;

BASE SEQUENCE; CARBON; CARBON ISOTOPES; DNA; DNA PROBES; ECOSYSTEM; EUKARYOTA; FUNGI; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PLANTS; SOIL; SOIL MICROBIOLOGY;

ASCOMYCOTA; CERCOZOA; ELEUTHERASCUS; EUKARYOTA; FUNGI; FUSARIUM; GALACTOMYCES; GIBBERELLA; MORTIERELLA; POLYMYXA; PROTISTA; PYTHIUM; STRAMENOPILES; SYNCEPHALIS;

EID: 84855256371     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2011.01224.x     Document Type: Article

References (36)

1. Asakawa S & Kimura M (2008) Comparison of bacterial community structures at main habitats in paddy field ecosystem based on DGGE analysis. Soil Biol Biochem 40: 1322-1329.
2. Asari N, Ishihara R, Nakajima Y, Kimura M & Asakawa S (2007) Succession and phylogenetic composition of eubacterial communities in rice straw during decomposition on the surface of paddy field soil. Soil Sci Plant Nutr 53: 56-65.
3. Bastian F, Bouziri L, Nicolardot B & Ranjard L (2009) Impact of wheat straw decomposition on successional patterns of soil microbial community structure. Soil Biol Biochem 41: 262-275.
4. 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ Microbiol 9: 752-764.
5. Boschker HTS & Middelburg JJ (2002) Stable isotopes and biomarkers in microbial ecology. FEMS Microbiol Ecol 40: 85-95.
6. Clarke KR & Gorley RN (2001) PRIMER-E. PRIMER-E Ltd, Plymouth, UK.
7. Díez B, Pedrós-Alió C, Marsh TL & Massana R (2001) Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl Environ Microbiol 67: 2942-2951.
8. 15N-DNA stable isotope probing. Fungal Ecol 4: 115-119.
9. Friedrich MW (2006) Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes. Curr Opin Biotechnol 17: 59-66.
10. Glissmann K, Weber S & Conrad R (2001) Localization of processes involved in methanogenic in degradation of rice straw in anoxic paddy soil. Environ Microbiol 3: 502-511.
11. Kimura M & Asakawa S (2006) Comparison of community structures of microbiota at main habitats in rice field ecosystems based on phospholipid fatty acid analysis. Biol Fert Soils 43: 20-29.
12. 4). Soil Biol Biochem 36: 1399-1416.
13. Kjøller AH & Struwe S (2002) Fungal communities, succession, enzymes, and decomposition. Enzymes in the Environment: Activity, Ecology, and Applications (Burns RG & Dick RP, eds), pp. 267-284. Marcel Dekker, New York, NY.
14. 13C-labeled plant residue in soil: analysis by a DNA-SIP approach. Soil Biol Biochem 43: 814-822.
15. Lu YH & Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309: 1088-1090.
16. Lueders T, Manefield M & Friedrich MW (2004) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol 6: 73-78.
17. Manefield M, Whiteley AS, Griffiths RI & Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68: 5367-5373.
18. Matsuyama T, Nakajima Y, Matsuya K, Ikenaga M, Asakawa S & Kimura M (2007) Bacterial community in plant residues in a Japanese paddy field estimated by RFLP and DGGE analyses. Soil Biol Biochem 39: 463-472.
19. 13C-labeled rice-straw-derived carbon into microbial communities in submerged rice field soil and percolating water. Soil Biol Biochem 38: 3483-3491.
20. Nakamura A, Tun CC, Asakawa S & Kimura M (2003) Microbial community responsible for the decomposition of rice straw in a paddy field: estimation by phospholipid fatty acid analysis. Biol Fert Soils 38: 288-295.
21. Pascault N, Cécillon L, Mathieu O, Hénault C, Sarr A, Lévêque J, Farcy P, Ranjard L & Maron PA (2010) In situ dynamics of microbial communities during decomposition of wheat, rape, and alfalfa residues. Microb Ecol 60: 816-828.
22. Poll C, Brune T, Begerow D & Kandeler E (2010) Small-scale diversity and succession of fungi in the detritusphere of rye residues. Microb Ecol 59: 130-140.
23. Radajewski S, Ineson P, Parekh NR & Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646-649.
24. Radajewski S, McDonald IR & Murrell JC (2003) Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr Opin Biotechnol 14: 296-302.
25. Robinson CH, Dighton J, Frankland JC & Roberts JD (1994) Fungal communities on decaying wheat-straw of different resource qualities. Soil Biol Biochem 26: 1053-1058.
26. 13C-labelled straw in the rice rhizosphere. Environ Microbiol Rep 3: 587-596.
27. Sugano A, Tsuchimoto H, Tun CC, Asakawa S & Kimura M (2005a) Succession and phylogenetic profile of eubacterial communities in rice straw incorporated into a rice field: estimation by PCR-DGGE analysis. Soil Sci Plant Nutr 51: 51-60.
28. Sugano A, Tsuchimoto H, Tun CC, Kimura M & Asakawa S (2005b) Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses. Archaea 1: 391-397.
29. Sugano A, Tsuchimoto H, Tun CC, Asakawa S & Kimura M (2007) Succession and phylogenetic profile of eukaryotic communities in rice straw incorporated into a rice field: estimation by PCR-DGGE and sequence analyses. Soil Sci Plant Nutr 53: 585-594.
30. Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
31. Thorn RG & Lynch MDJ (2007) Fungi and eukaryotic algae. Soil Microbiology, Ecology, and Biochemistry (Paul EA ed), pp. 145-162. Academic Press, Oxford.
32. Tun CC & Kimura M (2000) Microscopic observation of the decomposition process of leaf blade of rice straw and colonizing microorganisms in a Japanese paddy field soil during the cultivation period of paddy rice. Soil Sci Plant Nutr 46: 127-137.
33. Tun CC, Ikenaga M, Asakawa S & Kimura M (2002) Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis. Soil Sci Plant Nutr 48: 805-813.
34. van der Wal A, van Veen JA, Pijl AS, Summerbell RC & de Boer W (2006) Constraints on development of fungal biomass and decomposition processes during restoration of arable sandy soils. Soil Biol Biochem 38: 2890-2902.
35. Weber S, Lueders T, Friedrich MW & Conrad R (2001a) Methanogenic populations involved in the degradation of rice straw in anoxic paddy soil. FEMS Microbiol Ecol 38: 11-20.
36. Weber S, Stubner S & Conrad R (2001b) Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. Appl Environ Microbiol 67: 1318-1327.